smsMap: mapping single molecule sequencing reads by locating the alignment starting positions

DMSC: A Dynamic Multi-Seeds Method for Clustering 16S rRNA Sequences Into OTUs

(2019) Ze-Gang Wei et al.   Frontiers in Microbiology

Winfree loop sustained oscillation in two-dimensional excitable lattices: Prediction and realization

(2019) Yu Qian et al.   CHAOS

Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection

(2019) Themoula Charalampous et al.   NATURE BIOTECHNOLOGY

lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data

(2018) Ehsan Haghshenas et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

NPBSS: a new PacBio sequencing simulator for generating the continuous long reads with an empirical model

(2018) Ze-Gang Wei et al.   BMC BIOINFORMATICS

Fast and efficient short read mapping based on a succinct hash index

(2018) Haowen Zhang et al.   BMC BIOINFORMATICS

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

DBH: A de Bruijn graph-based heuristic method for clustering large-scale 16S rRNA sequences into OTUs

(2017) Ze-Gang Wei et al.   JOURNAL OF THEORETICAL BIOLOGY

DMclust, a Density-based Modularity Method for Accurate OTU Picking of 16S rRNA Sequences

(2017) Ze-Gang Wei et al.   Molecular Informatics

Fast and sensitive mapping of nanopore sequencing reads with GraphMap

(2016) Ivan Sović et al.   Nature Communications

rHAT: fast alignment of noisy long reads with regional hashing

(2015) Bo Liu et al.   BIOINFORMATICS

MtHc: a motif-based hierarchical method for clustering massive 16S rRNA sequences into OTUs

(2015) Ze-Gang Wei et al.   Molecular BioSystems

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data

(2015) Judith Risse et al.   GigaScience

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

(2014) Philip M Ashton et al.   NATURE BIOTECHNOLOGY

Building Phylogenetic Trees from Molecular Data with MEGA

(2013) B. G. Hall   MOLECULAR BIOLOGY AND EVOLUTION

The Database of Genomic Variants: a curated collection of structural variation in the human genome

(2013) Jeffrey R. MacDonald et al.   NUCLEIC ACIDS RESEARCH

De Novo Transcriptome Sequence Assembly and Analysis of RNA Silencing Genes of Nicotiana benthamiana

(2013) Kenlee Nakasugi et al.   PLoS One

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

The GEM mapper: fast, accurate and versatile alignment by filtration

(2012) Santiago Marco-Sola et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Using quality scores and longer reads improves accuracy of Solexa read mapping

(2008) Andrew D Smith et al.   BMC BIOINFORMATICS